====== Setting up FSL ======

  * For reference, the FSL-FEAT analysis **guide** is available at [[http://www.fmrib.ox.ac.uk/fsl/feat5/]]
  * A **glossary** containing descriptions of the output files from FSL-FEAT is available at [[http://www.fmrib.ox.ac.uk/fsl/feat5/index.html]]





===== Logging in to Golgi =====
Go [[biac:connect_to_golgi:setting_up_f-secure_profile|this page]] for instructions for setting up your **Golgi Profile**. Checking to make sure that everything is set up correctly will save you much aggravation.

Run "Xwin32" from the Start Menu. An "X" will appear in the icon tray on the taskbar.
Run “F-Secure SSH Client” from the Start menu. In the F-Secure window, select profiles->Golgi. Enter your Golgi password.  


===== Organizing Your Data =====
  - In Huxley/Data/Class.01/Students create a folder for yourself.  It is helpful to keep open a Windows Explorer window of your Class.01/Students directory we will be working with.
  - From Huxley/Data/Class.01/Examples __COPY, DO NOT CUT!!!__ **ANAT_4** and **FUNC_4/Run1_Block** and paste them in your folder, renaming them **Anat** and **Func**  
  - Create a new folder called **FSL** in your home directory


=====Preparing Your Data for Analysis=====
** Note that on Linux/Unix systems, capitalization matters! Make sure that you correctly capitalize directory and file names.**
  - Open a new window in golgi 
     - type **cifslogin //huxley/data**
     - type **cd /CIFS/Huxley/Data/Class.01/Students/**
  - Change into your folder (e.g., **cd myfoldername**) then change into **Anat**.
  - To create the NIFTI files for the anatomical data: <code>bxh2analyze --niftihdr -s -v ANAT4_Coplanar.bxh anat01</code>
  - This will make 3 files: **anat01.bxh, anat01.hdr, and anat01.img**.
  - Next, go into the directory with your functional run (e.g., **cd ../Func**).
  - To create the NIFTI files for the functional data: <code>bxh2analyze --niftihdr -s -v FUNC4_V.bxh run1</code> 
  - This will make 3 files: **run1.bxh, run1.hdr, and run1.img**

=====Extracting the Brain=====
**This removes the surrounding skull and tissue from the anatomical images.**
  - In Golgi type: **fsl &**
  - This will bring up a GUI, click **BET Brain Extraction**
  - For the input image select the **anat01.hdr** file.
  - **Generate image with non-brain matter removed** should be the only checked option.
  - Click **ok**.
  - This should take about 1 minute to run. When it finishes, you will have a new file in the Anat directory: "anat01_brain.nii.gz". You should view this file in MATLAB using **showsrs2**, to see the effects of brain extraction. 

=====Help for Problems with FSL=====
Some, but not all, individuals have reported receiving a **"DISPLAY is not set..."** error when attempting to start FSL. We are working to diagnose exactly what settings are leading to this error. The following seem to be workarounds:
  - Starting a new GOLGI window (keeping your original one open) and loading from that second window.
  - Starting FSL from the root directory. 

See your TA for help with these, if it doesn't work for you.


====== Running FSL Analyses ======
** We'll begin with a first-level analysis (i.e., on only one run of one subject's data).**
  - Within your FSL folder, create an empty folder named **run01**.
  - Move (don't just copy) the run1.img, run1.bxh, and run1.hdr files you just created into that folder. Also move the anat01_brain.nii.gz file into that folder.

  $ mv run1.* ./../FSL/run01
  $ cd ../Anat
  $ mv anat01_brain.nii.gz ./../FSL/run01

  - In golgi, change into the fsl\run01 folder.
  - If FSL is not already open, type **fsl &** and click **FEAT FMRI Analysis** in the GUI. Just click once; it will take a few seconds to appear.
  - Go to this webpage - [[http://www.fmrib.ox.ac.uk/fsl/feat5/detail.html]] - and follow along to read about each setting you are changing

===== FSL GUI settings =====
  - **Pull-down menus**
    * At top, the left menu should read **First-level analysis**. The right menu should read **Full analysis**.
  - **Misc** tab
    * Click on this tab. You should leave everything on this tab at the default settings.
  - **Data** tab
    * Click on this tab, next.
    * Make sure that **Number of Analyses** is set to **1**. 
    * Click **Select 4D Data**, go to the **run01** folder, and select the **run1.hdr** file that you created earlier. Click **OK** twice, ignoring any error messages at this stage.
    * Click **Select Output Directory**, again go to the **run01** folder, and click **OK**. 
    * Check to make sure your **Total volumes** is set to **131** (should have changed when you selected your func data)
    * Set the **TR(s)** to **2**. This is your repetition time (TR) in seconds.
    * You shouldn't have to change anything else. The defaults should be correct: **Delete Volumes = 0, High-Pass Filter cutoff (s) = 100**.
  - Prestats Tab 
    * **Motion correction** should be **MCFLIRT**
    * **B0 unwrapping** should be unchecked (gray)
    * **Slice timing correction** should be **Interleaved**
    * **BET brain extraction** should be checked (yellow)
    * **Spatial smoothing** should be set to **8mm**
    * **Intensity normalization** should be unchecked (gray)
    * **Temporal filtering** should be **Highpass**
    * **Melodic ICA** should be unchecked (gray).
  - Stats Tab
    * **Use FILM prewhitening** should be checked
    * **Add motion parameterers** should be **No**
    * Ignore **Full model setup**, for now. We'll come back to this in a moment.
  - Post-Stats Tab
    * The key part of this is **Thresholding**. From left to right, it should read **Cluster**, ** Z Threshold 2.3**, and **Cluster P threshold 0.05**.
  - Registration Tab
    * **Standard space** should already be checked, with the file **/usr/local/packages/fsl/etc/standard/avg152T1_brain.hdr**, **Normal Search**, and **12 DOF**.
    * Click the **Main structural image** checkbox. Select your **anat01_brain.nii.gz** file and then click **OK**. You should have **Normal Search** and **7 DOF** selected automatically.


Now leave FSL open, we will come back to it after we set up the design.


===== Setting up your Design =====
This is the part of analysis where you specify what happened in the experiment. For your reference, here is the description of the experimental paradigm:

  * A static checkerboard is displayed for the first two TRs (4s). 
  * Alternating blocks of flashing and static checkerboards begin with the third TR. The first block displays a flashing checkerboard for 10 TRs (20s).  The second block displays a static checkerboard for 10 TRs (20s).  
  * This set of flashing/static blocks is repeated six times: F-S-F-S-F-S-F-S-F-S-F-S.  
  * After the final static block, another 6 TRs (12s) of flashing checkerboard appeared before the run ended. 
  * The subject tapped his/her fingers repeatedly whenever the checkerboard was flashing.

You need to create a **three-column text file** that describes your experimental paradigm. Each line of the file consists of three values, separated by tabs. 
  * The three columns are: **Start of event (seconds)**, **Duration of event (seconds)**, and **Intensity of event**. 
  * So, for the first row of the text file, we could use: 
<code>4     20       1</code>
  * You need to create a text file that has seven rows, each corresponding to one of the blocks of visual stimuli. Save this file in your **FSL** directory as **block_3col.txt**.

Now, you can go back to the **Stats** tab, and then click on **Full model setup**. 
  * In this experiment, only one thing happens: a checkerboard flashes. So, we only need one **Explanatory Variable (EV)**. Type **Flash** into the **EV name** field.
  * On the **Basic shape** pull-down menu, select **Custom (3 column format)**. When the **Filename** box pops up, select the **block_3col.txt** file that you just created.
  * On the **Convolution** pull-down menu, select **Double-Gamma HRF**. Leave **Phase** at **0** seconds. 
  * **Add temporal derivative** should be unchecked (gray).
  * **Apply temporal filtering** should be checked (yellow).

You can now click on **View Design**, and you should see something that looks like the predicted hemodynamic changes that should follow alternating blocks of activation and deactivation. Close the window that just popped up (not your main FSL window), and hit "Done".


===== Running FSL (First-level analysis)=====
You are now ready to run a first-level analysis (i.e., one run of one subject).

  - Click the **save** button. Go to your **/FSL** directory. Save it as **template.fsf**; you'll need to type that file name at the end of the **selection** box.

If you are doing this as a class exercise, **FIND YOUR TA AND TELL HIM/HER YOU ARE READY**. Then, you can hit **GO**. The **FEAT Watcher** window should pop up; this lets you follow the progress of your analysis. Be patient and you should see FEAT begin running. This generally takes about 1 hour to completely analyze the one run.


====== Looking at your FSL analyses ======
FSL creates HTML pages for your output; these can be viewed in Internet explorer or any other browser.
  - Open your **FEAT report** by entering the run#.feat folder that should be located in the run# folder.
  - Compare your FEAT report to the one in Students/Example/FSL/Run#

You can also view the FSL output using ShowSrs2.
  - In the **Reg** subdirectory that was created, load the hires.nii file for your anatomical image. 
  - To get your analyzed data, go to the **Stats** subdirectory and load the zstat1.nii image (or similar).
  - The anatomical image is has 256*256*21 voxels; the functional image has 64*64*21 voxels.